Contacts of the helix formed by residues 302 - 327 (chain U) in PDB entry 3EXG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 302 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1U PHE* 3.3 17.9 - - - -
296U VAL* 4.0 3.4 - - - -
301U ALA* 1.3 74.8 - - - +
303U VAL* 1.3 67.5 + - - +
304U GLU* 2.9 23.9 + - - +
305U GLU* 3.1 32.3 + - - +
306U LEU* 3.2 13.3 + - - +
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Residues in contact with VAL 303 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2066 HIS* 6.4 2.2 - - + -
292U LYS* 3.3 33.2 - - - +
296U VAL* 3.7 19.4 - - + +
302U SER* 1.3 72.4 - - - +
304U GLU* 1.3 81.5 + - + +
306U LEU* 3.6 4.9 + - - +
307U LYS* 3.0 29.8 + - + +
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Residues in contact with GLU 304 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2056 THR* 6.1 0.7 - - - +
302U SER* 2.9 24.3 + - - +
303U VAL* 1.3 98.1 + - + +
305U GLU* 1.3 60.2 + - - +
307U LYS* 3.6 5.8 + - - +
308U GLU* 2.9 43.5 + - - +
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Residues in contact with GLU 305 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1U PHE* 3.3 6.1 - - + -
29U ARG* 2.8 30.1 + - - -
33U LEU* 4.1 14.5 - - - +
301U ALA* 3.1 29.2 - - - +
302U SER* 3.1 25.0 + - - +
304U GLU* 1.3 78.4 - - - +
306U LEU* 1.3 61.2 + - + +
308U GLU* 3.4 11.9 + - - +
309U ILE* 3.1 32.7 + - + +
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Residues in contact with LEU 306 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33U LEU* 4.4 4.3 - - + -
36U TYR* 3.7 39.5 + - + +
292U LYS* 3.7 42.8 - - + +
295U MET* 4.3 23.1 - - + -
296U VAL* 4.5 11.0 - - + -
301U ALA* 4.3 12.1 - - + -
302U SER 3.2 15.1 + - - +
303U VAL* 3.9 3.6 - - - +
305U GLU* 1.3 78.3 - - + +
307U LYS* 1.3 60.9 + - - +
308U GLU 3.1 0.2 - - - -
309U ILE* 3.0 31.4 + - + +
310U ASP* 3.0 17.1 + - - -
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Residues in contact with LYS 307 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2056 THR* 3.5 28.1 + - + +
2066 HIS* 5.2 9.2 + - + +
2556 LYS* 3.0 25.9 + - - +
2566 THR* 4.6 1.2 + - - +
2576 ASN* 3.9 18.3 + - - -
292U LYS* 5.8 3.7 - - - +
303U VAL* 3.0 22.3 + - + +
304U GLU* 3.9 7.0 - - - +
306U LEU* 1.3 76.2 - - - +
308U GLU* 1.3 59.4 + - + +
310U ASP* 3.4 32.3 - - - +
311U VAL* 3.4 16.1 - - - +
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Residues in contact with GLU 308 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2056 THR* 6.2 4.3 - - + -
304U GLU* 2.9 35.3 + - - +
305U GLU* 3.5 9.0 - - - +
306U LEU 3.1 0.2 - - - -
307U LYS* 1.3 75.1 - - + +
309U ILE* 1.3 60.7 + - + +
310U ASP 3.3 0.2 - - - -
311U VAL* 3.3 12.1 + - + +
312U GLU* 3.1 35.3 + - + +
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Residues in contact with ILE 309 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33U LEU* 4.3 28.5 - - + +
36U TYR* 4.2 11.7 - - + -
37U ARG* 3.6 54.5 - - + +
40U GLN* 5.7 0.2 - - + -
305U GLU* 3.1 18.0 + - + +
306U LEU* 3.0 26.3 + - + +
308U GLU* 1.3 74.4 - - + +
310U ASP* 1.3 65.6 + - - +
312U GLU* 3.3 9.5 + - - +
313U VAL* 2.9 24.6 + - + +
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Residues in contact with ASP 310 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36U TYR* 2.9 26.0 + - - -
40U GLN* 3.0 32.6 - - - +
44U ARG* 5.9 0.2 - - - -
306U LEU 3.0 4.5 + - - -
307U LYS* 3.4 38.4 - - + +
309U ILE* 1.3 76.7 - - - +
311U VAL* 1.3 58.7 + - + +
313U VAL* 3.3 5.0 + - - +
314U ARG* 2.8 33.1 + - - +
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Residues in contact with VAL 311 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2546 MET 4.2 16.4 - - - +
2556 LYS* 3.9 38.8 - - + +
2876 PHE* 5.6 0.5 - - - -
307U LYS* 3.4 22.2 - - - +
308U GLU* 3.3 12.5 + - + +
309U ILE 3.2 0.6 - - - -
310U ASP* 1.3 73.1 - - - +
312U GLU* 1.3 68.8 + - + +
314U ARG* 3.2 4.0 + - - +
315U LYS* 3.0 26.0 + - + +
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Residues in contact with GLU 312 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37U ARG* 3.2 36.1 + - - +
308U GLU* 3.1 21.8 + - - +
309U ILE* 3.5 11.7 - - - +
311U VAL* 1.3 76.9 - - + +
313U VAL* 1.3 63.1 + - - +
315U LYS* 3.4 7.6 + - - +
316U GLU* 3.1 21.4 + - - +
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Residues in contact with VAL 313 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37U ARG* 4.0 27.1 - - + +
40U GLN* 3.7 9.9 - - + +
41U THR* 3.7 36.1 - - + +
44U ARG* 3.6 28.0 - - + -
309U ILE* 2.9 24.4 + - + +
310U ASP* 3.6 4.9 - - - +
312U GLU* 1.3 75.6 - - - +
314U ARG* 1.3 59.0 + - - +
316U GLU* 2.8 25.2 + - + +
317U ILE* 2.8 15.9 + - + +
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Residues in contact with ARG 314 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2576 ASN* 3.8 15.2 - - - +
2866 ASN 3.3 15.4 + - - -
2876 PHE* 3.2 51.8 + - + +
2886 LEU 4.4 1.0 + - - -
2896 ASP* 3.0 28.3 + - - -
44U ARG* 3.2 53.8 - - + +
310U ASP 2.8 20.7 + - - +
311U VAL* 4.1 3.6 - - - +
313U VAL* 1.3 74.7 - - - +
315U LYS* 1.3 60.6 + - - +
317U ILE* 3.9 7.8 - - - +
318U GLU* 3.2 31.0 + - - +
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Residues in contact with LYS 315 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2546 MET* 5.9 6.3 - - - -
2876 PHE* 4.2 16.7 - - + -
311U VAL* 3.0 18.5 + - + +
312U GLU* 3.8 5.6 - - - +
314U ARG* 1.3 75.7 - - - +
316U GLU* 1.3 67.8 + - - +
318U GLU* 3.1 4.1 + - + +
319U ASP* 3.0 60.1 + - - +
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Residues in contact with GLU 316 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41U THR* 5.9 4.9 - - + -
102U VAL* 5.5 11.9 - - + -
312U GLU 3.1 14.6 + - - +
313U VAL* 2.8 16.9 + - + +
315U LYS* 1.3 78.4 - - - +
317U ILE* 1.3 60.6 + - + +
319U ASP* 3.5 12.1 + - - +
320U ALA* 3.3 22.3 + - - +
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Residues in contact with ILE 317 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41U THR* 4.2 8.3 - - + +
44U ARG* 3.5 30.5 - - + +
45U MET* 3.8 16.8 - - + +
48U LYS* 3.7 38.8 - - + -
102U VAL* 3.5 33.7 - - + -
106U LEU* 4.9 1.8 - - + -
313U VAL* 2.8 19.7 + - + +
314U ARG* 4.0 7.2 - - - +
316U GLU* 1.3 71.6 - - + +
318U GLU* 1.3 64.9 + - - +
320U ALA* 3.3 3.1 - - - +
321U ALA* 2.8 28.4 + - - +
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Residues in contact with GLU 318 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2836 PRO 5.4 1.6 - - - +
2866 ASN* 2.8 28.2 + - - +
2876 PHE* 3.7 27.2 - - + -
48U LYS* 2.8 36.4 + - - -
314U ARG* 3.2 26.1 + - - +
315U LYS* 3.1 5.4 + - + +
317U ILE* 1.3 83.9 - - - +
319U ASP* 1.3 58.5 + - - +
321U ALA* 4.1 2.5 - - - +
322U GLN* 3.1 26.0 + - - +
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Residues in contact with ASP 319 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103U ARG* 5.0 9.3 + - - +
315U LYS* 3.0 51.6 + - - +
316U GLU* 3.9 12.2 - - - +
318U GLU* 1.3 74.5 - - - +
320U ALA* 1.3 61.2 + - - +
322U GLN* 3.2 13.7 + - - +
323U PHE* 2.9 28.9 + - - +
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Residues in contact with ALA 320 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102U VAL* 4.1 24.7 - - + -
103U ARG* 4.2 30.0 - - + +
106U LEU* 4.1 6.1 - - + -
316U GLU 3.3 12.4 + - - +
317U ILE 3.3 9.4 - - - +
319U ASP* 1.3 78.1 - - - +
321U ALA* 1.3 58.6 + - - +
323U PHE* 2.8 8.8 + - - +
324U ALA* 2.8 26.7 + - - +
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Residues in contact with ALA 321 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48U LYS* 3.6 39.9 - - + +
52U LEU* 4.5 6.3 - - + -
106U LEU* 3.5 12.0 - - + +
317U ILE 2.8 20.4 + - - +
318U GLU* 4.1 3.6 - - - +
320U ALA* 1.3 72.8 - - - +
322U GLN* 1.3 63.1 + - - +
324U ALA* 4.1 3.4 - - - -
325U THR* 2.9 30.6 + - + +
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Residues in contact with GLN 322 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103U ARG* 5.9 1.2 - - - +
318U GLU 3.1 18.0 + - - +
319U ASP* 3.2 17.0 + - - +
321U ALA* 1.3 76.2 - - - +
323U PHE* 1.3 73.3 + - - +
325U THR* 3.4 8.2 + - - +
326U ALA* 3.3 29.7 + - - +
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Residues in contact with PHE 323 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103U ARG* 3.3 61.2 - - + +
107U ALA* 4.0 19.3 - - + -
114U GLY* 4.6 13.2 - - - -
319U ASP 2.9 12.3 + - - +
320U ALA 2.8 10.0 + - - +
322U GLN* 1.3 89.2 - - - +
324U ALA* 1.3 67.8 + - - +
326U ALA* 3.4 1.0 + - - -
327U ASP* 3.0 45.0 + - + +
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Residues in contact with ALA 324 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52U LEU* 5.6 1.6 - - + -
103U ARG 4.8 0.2 - - - +
106U LEU* 3.8 17.9 - - + +
107U ALA* 3.7 30.7 - - + +
110U THR* 3.0 23.4 + - + +
112U ARG* 3.4 15.4 + - - +
320U ALA 2.8 14.4 + - - +
321U ALA* 3.7 6.1 - - - +
323U PHE* 1.3 86.4 - - + +
325U THR* 1.3 58.5 + - + +
326U ALA 3.6 0.3 + - - -
327U ASP* 3.9 0.4 + - - -
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Residues in contact with THR 325 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3284 ASN* 5.9 3.6 - - - +
52U LEU* 3.7 31.9 - - + -
57U ILE* 4.3 15.9 - - + -
110U THR* 4.8 1.6 - - + -
112U ARG* 3.1 20.0 + - - +
321U ALA* 2.9 22.5 + - + +
322U GLN* 3.4 9.7 + - - -
324U ALA* 1.3 76.5 - - - +
326U ALA* 1.3 60.2 + - - +
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Residues in contact with ALA 326 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322U GLN* 3.3 26.4 + - - +
323U PHE* 3.8 1.3 - - - +
325U THR* 1.3 80.1 + - - +
327U ASP* 1.3 64.5 + - - +
328U PRO* 3.7 4.3 - - - +
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Residues in contact with ASP 327 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107U ALA* 5.0 0.6 - - + +
112U ARG* 3.1 42.8 + - + +
113U LYS* 3.7 10.4 + - - +
114U GLY* 2.9 36.6 + - - -
323U PHE* 3.0 33.8 + - + +
324U ALA* 3.9 1.5 + - - +
325U THR 3.5 0.6 - - - -
326U ALA* 1.3 79.5 - - - +
328U PRO* 1.3 91.8 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il